System Storage Full

I have a jailbroken iPhone 4 and use Cydia, SBSettings and iFile to see how much storage is marked as Free between the two partitions on my device.

The problem is, my System Storage had a total size of 1GB and is 100% full.

SBSettings says this in addition to Cydia, but when I check the size of the System folder with iFile, then I see that all files together are not more then 640MB.

Shouldn't I still have 360MB of free space on my System Storage?

I checked the content and sizes of the folders with another iPhone 4 with the same iOS version and all the folders are exactly the same size, and that iPhone does not have this problem. This problem is blocking me from installing updates and packages from Cydia.

"System Storage" refers to everything mounted on /, which is more than just /System. Cydia and SBSettings are not lying to you. The only way you can fix this is by removing packages in Cydia that take up System Storage, or restore with a custom IPSW that makes the System partition larger.

See Where is the dividing line (mount point) of the two iOS partitions?

Another solution (if you have SSH and SFTP access to the iPhone) is to symbolic link some stuff from the system partition to the user partition. It's dangerous, but if you know what you're doing, it can save you some time. Always back up first.